AUSTRALIAN forces in Afghanistan have halted joint patrols alongside Afghan forces amid concerns a controversial film on Islam made in the US could spark more "green on blue" attacks by local soldiers.

The decision came after International Security Assistance Force (ISAF) commander General John Allen directed all allied forces to suspend joint activities below kandak (battalion) level.

It also follows a rise in insider attacks and a surge in violence and protests across the Middle East in response to the film, Innocence of Muslims, which many view as deeply insulting to the Prophet.

But Defence Minister Stephen Smith said today the ISAF directive would not halt all partnered activities in Afghanistan.

Missions involving more than 500 troops would continue and smaller operations at company and platoon level will require the approval of the relevant regional commander.

Because of this film, it's crucial that we just take a deep breath and maybe take a little step for a moment to let that subside

Mr Smith told parliament that no joint patrols below kandak level involving Australian troops had been conducted on Monday and Tuesday.

But Australian and Afghan National Army (ANA) commanders were holding talks about making a case to resume joint patrols.

"I am not putting a timetable on that," Mr Smith said.

"That will be an operational matter.

"In the meantime all commanders have been asked to review forces protection measures and to minimise risk against these so-called insider incidents."

Seven Australian soldiers have died in three attacks by rogue ANA soldiers, and on August 29 three were shot and killed in a single incident.

Australian Greens leader Christine Milne said there was no justification for Australian troops to remain in Afghanistan.

The government had justified the mission on the grounds it needed to mentor Afghan forces to take over security once Australian forces departed in 2014, but was now saying they were not to be trusted.

All commanders have been asked to minimise risk against these so-called insider incidents

"It makes no sense - we need to bring our troops home as quickly and as safely as possible," she told reporters.

Government Senate leader Chris Evans said the ISAF directive was temporary and didn't undermine the mission.

"I am not sure that there is anything in the events of the last few days that would cause us to review our fundamental commitment to Afghanistan or our plans for transitioning to local Afghan command of operations," he told the Senate.

Opposition defence spokesman David Johnston said a short term pause was needed to allow the outrage over the film to subside.

"Because of this film, it's crucial that we just take a deep breath and maybe take a little step for a moment to let that subside," he told reporters.

"We have all been to funerals recently (and) these green on blue events are just something we have to get a handle on."